Are my steps correct for a proper classification of a sick brain?
It looks like everything you want is available with the Deep Learning Toolkit (DLTK) for Medical Imaging

There is also a blog: An Introduction to Biomedical Image Analysis with TensorFlow and DLTK

There is a DataCamp course that walks you through most of the process but instead of a classifier they use deep learning to reconstruct brain images.  They provide a link to their MNIST classifier example which should be easy to adapt for your purpose.  See: Reconstructing Brain MRI Images Using Deep Learning (Convolutional Autoencoder)

ResearchGate has a thread that may help:
What is the appropriate way to use Nifti files in deep learning?